I am using shadowbox.js and the default xy is 00 so the shadowbox opens in the very center of the page. Is there any way to change the coordinates in the .js file to customize where the box opens on the screen.
here's the catch - i can't offer you any solutions as to why yours doesn't seem to be working if i can't see a relatively simple example of your broken implementation... :-/
what i would recommend is to take a basic example of theirs and make a simple plain test page on your site (just with one shadow box on the page) - get theirs working there, and then start to swap in your content and fix it in small increments. then, once you have your content working in their shadowbox example, integrate that into your larger page that you just sent here...
if you get stuck along the way, point us to your test page and we can see what suggestions we can offer.